Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
965,365 |
T→C |
M174T (ATG→ACG) |
ycaQ → |
winged helix DNA‑binding protein YcaQ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 965,365 | 0 | T | C | 100.0%
| 62.7
/ NA
| 18 | M174T (ATG→ACG) | ycaQ | winged helix DNA‑binding protein YcaQ |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (10/8); total (10/8) |
AGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGATGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATC > NZ_CP009273/965278‑965445
|
aGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAggtgacggt > 1:809503/1‑91 (MQ=255)
aGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGgcgc < 1:154138/91‑1 (MQ=255)
gTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCaa > 1:855423/1‑91 (MQ=255)
gCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACt > 2:237070/1‑91 (MQ=255)
cATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCAcc < 1:473262/91‑1 (MQ=255)
cATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCAcc < 1:136529/91‑1 (MQ=255)
aaCGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCgtgt < 2:809503/91‑1 (MQ=255)
cATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGc > 1:63264/1‑91 (MQ=255)
cATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGc > 1:192782/1‑91 (MQ=255)
cATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGc > 2:666829/1‑91 (MQ=255)
aTCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGcc < 1:71153/91‑1 (MQ=255)
ggAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGAc < 2:435931/91‑1 (MQ=255)
ttatttaCTGCCGGAAAGGAGACGGTGATTGAACGCCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGgatg > 2:828465/1‑91 (MQ=255)
ttaCTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGAtgatga < 2:639795/91‑1 (MQ=255)
aCTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAgc < 2:284663/91‑1 (MQ=255)
cTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAgcg > 1:561415/1‑91 (MQ=255)
tGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAgcgc > 1:211180/1‑91 (MQ=255)
tGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAgcgc > 2:639206/1‑91 (MQ=255)
ggAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGAtc > 1:857148/1‑91 (MQ=255)
|
AGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGATGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATC > NZ_CP009273/965278‑965445
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGATGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCA > NZ_CP009273/965268‑965465
|
GCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGT > SRR3722118.827304/1‑101 (MQ=60)
TTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTG < SRR3722118.873117/101‑1 (MQ=60)
TGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAAC < SRR3722118.124318/101‑1 (MQ=60)
CCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAA > SRR3722118.874405/1‑101 (MQ=60)
TCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACNGCNNNTGGAAGGTTTATNNNNNNNNNNNNAGGTGACGGTGATTGAACGGCGCAAAT > SRR3722118.601838/1‑101 (MQ=60)
AGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGC < SRR3722118.157117/101‑1 (MQ=60)
GCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGC > SRR3722118.196598/1‑101 (MQ=60)
GCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGC > SRR3722118.64442/1‑101 (MQ=60)
CATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCC < SRR3722118.139124/101‑1 (MQ=60)
CATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCC < SRR3722118.483257/101‑1 (MQ=60)
ATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGAT < SRR3722118.72471/101‑1 (MQ=60)
GGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCG > SRR3722118.573313/1‑101 (MQ=60)
GTTTATTTAGTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCtgtctcttatacacatctccgagcccacgagacggactcctatctcgtatgcc > SRR3722118.852673/1‑48 (MQ=60)
GTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGC > SRR3722118.215421/1‑101 (MQ=60)
ATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATC > SRR3722118.876177/1‑101 (MQ=60)
CGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCA > SRR3722118.561226/1‑101 (MQ=60)
|
GCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGATGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCA > NZ_CP009273/965268‑965465
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
